A senior undercover CIA officer, accused by the spy agency of "war crimes", has alleged that it halted an internal investigation that could have exonerated him and placed him under surveillance instead.

It does not name the operative. Nor does it list the crimes that the officer, who is said to still be a serving official, is alleged to have committed. The officer wants the CIA's inspector general to finish investigating – if only to be exonerated.

The lawsuit does not make any charges about the veracity of the alleged crimes, which the suit says also involves other CIA agents. The officer, named in the suit as John Doe, seeks the court to compel the CIA's inspector general to complete an investigation into Doe's involvement in the incident that the internal watchdog began around 2010 or 2011 and "unreasonably and intentionally delayed".

A spokesman for the CIA, Preston Golson, declined all comment about the allegations.

It is not clear what the crimes may have been. But it was during that period that the Justice Department began investigating CIA operatives for their involvement in the agency's Bush-era torture programs. The Justice Department announced in March 2011 it was dropping nearly all the torture investigations without bringing charges.

"Following a specific overseas assignment/activity, John Doe was wrongfully accused of participating in, committing and/or possessing information about war crimes," the lawsuit reads. "Other CIA employees were also accused."

"In connection with internal investigations of John Doe, CIA employees, either with or without authority, initiated physical and electronic surveillance of him, some of which were unlawful," the lawsuit alleges.

"The surveillance included harassment tactics undertaken by local law enforcement who were cooperating with the CIA. Other tactics involved corruption of electronic devices such as computers and cellphones. The Federal Bureau of Investigation opened an investigation into CIA's activities involving John Doe."

It adds: "A criminal inquiry was also opened and investigated by the Department of Justice. Without ever interviewing John Doe the matter was closed and prosecution was declined in or around 2011 – 2012," the lawsuit charges.

All the lawsuit says about John Doe's identity is that he is a "former member of the US armed forces and currently serves as a covert paramilitary officer" for the CIA. From 2002-2011 John Doe repeatedly deployed overseas for missions including "offensive operations against individuals designated or viewed as enemies of the United States".

John Doe wants the court to compel the CIA inspector general to complete the stalled investigation, which Doe alleges has stalled his career. The inspector general's office, Doe alleges, is "purposefully refusing to administratively close its investigation in order to discredit or otherwise cause harm to [Doe's] career".